Fasta name changes

[aniben]

I have a word file with 222 pages worth of fasta genes... that adds up. The phylogenetic program I plan to use doesn't like a long FASTA header all that much, so I have to change it to something less than 10 characters. considering the large number of genes I have in the document, I would like to know a way to change all these names in a quicker manner than just manually changing each and every one. I'm aware that building a program can solve this, but I only have introductory experience in python. Any advice? Thanks!

[rhinoceros]

First of all, you should not have sequence data in a word file. That is just asking for trouble. Second, you can easily edit the fasta headers in the *nix command line, given that your sequences are in a plain text file. So put your seqs into a proper text file and then post example headers and what you want them to look like..

[dariober]

I have a word file with 222 pages worth of fasta genes...

Do you mean MS Word document? If so, save it as text file. When asked, use "LF only" as newline character. As an aside, don't keep sequence or any other sort of data in Word documents, you are going to make your bioinformatic life really complicated with that!

The phylogenetic program I plan to use doesn't like a long FASTA header all that much, so I have to change it to something less than 10 characters.

Are you sure only 10 characters are allowed? That sounds a bit weird... Anyway, if you really want to cut sequence names short you could use this crude way:

awk '{if($0 ~ /^>/){x= substr($0, 1, 10); print x} else {print $0}}' seq.fa.txt > shortnames.fa

Replace 10 with the desired number of chars to keep, seq.fa.txt is the text file saved as above.

[Brian Bushnell]

With BBTools:

bbrename.sh in=old.fasta out=new.fasta

That will rename the reads as 1, 2, 3, 4, ... 222.

You can also give a custom prefix if you want. The input has to be text format, not .doc.

[aniben]

Ok, thanks. Making it to a text file won't be all that much of a problem.

[GenoMax]

As you make these changes keep in mind that those 10 characters have to be unique (and logical enough for you to understand the trees afterwards) otherwise the phylogenetic program may not like it.

How many sequences do you have in that file? Are they all unique? It may be easier to name them 1,2,3 .. based on Brian's suggestion and then convert back to real names once you complete the analysis (photoshop?)

[GenoMax]

Are you sure only 10 characters are allowed?

Some established phylogenetic programs (phylip) do have this requirement.